Sardine populations worldwide can fluctuate drastically over short time periods, in terms of both biomass and biological characteristics. Fluctuations might be amplified by pathogens, but such hypotheses have never been considered in the absence of clear macroscopic symptoms. In the Gulf of Lions (NW Mediterranean), an enduring severe decrease in sardine (Sardina pilchardus) size, condition and age has been observed since 2008, resulting in a strong decline in landings. This situation might have been caused or aggravated by diseases, especially as other drivers such as fisheries are not expected to be important. Therefore, we developed and performed a general veterinary study, aimed at detecting a wide range of potential pathogens, including parasites, viruses and bacteria. We explored which infectious agents are most likely to produce a causal relationship with sardine health, important information for future infection experiments. Among about 1300 sardines sampled during June 2014-July 2015, microscopic parasites (often trematodes and coccidians) and bacteria Tenacibaculum and Vibrio spp. were found. However, no clear damage to tissue was observed and there was generally no link between the agents' presence and host size or condition, so that no strong indications of pathogenicity were present. Nonetheless, 54 % of the sardines analysed in 2015 had elevated quantities of melano-macrophage centres (macrophage aggregates), indicating stress on the fish that might potentially be related to starvation and/or pollution.